| Chain sequence(s) |
D: TSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFAQSIISTLT
input PDB |
| Selected Chain(s) | D |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | No |
| alphaCutter usage | No |
| Dynamic mode | No |
| Automated mutations | Yes |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:11)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:11)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with D chain(s) selected (00:00:11)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:11)
[INFO] FoldX: Starting FoldX energy minimization (00:00:12)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:02:46)
[INFO] AutoMut: Residue number 91 from chain D and a score of 1.270 (valine) selected for
automated mutation (00:02:47)
[INFO] AutoMut: Residue number 19 from chain D and a score of 0.930 (leucine) selected for
automated mutation (00:02:47)
[INFO] AutoMut: Residue number 104 from chain D and a score of 0.814 (methionine) selected
for automated mutation (00:02:47)
[INFO] AutoMut: Residue number 92 from chain D and a score of 0.254 (isoleucine) selected
for automated mutation (00:02:47)
[INFO] AutoMut: Residue number 23 from chain D and a score of 0.230 (methionine) selected
for automated mutation (00:02:47)
[INFO] AutoMut: Residue number 94 from chain D and a score of 0.164 (leucine) selected for
automated mutation (00:02:47)
[INFO] AutoMut: Mutating residue number 91 from chain D (valine) into glutamic acid (00:02:47)
[INFO] AutoMut: Mutating residue number 91 from chain D (valine) into aspartic acid (00:02:47)
[INFO] AutoMut: Mutating residue number 19 from chain D (leucine) into glutamic acid (00:02:47)
[INFO] AutoMut: Mutating residue number 91 from chain D (valine) into arginine (00:02:54)
[INFO] AutoMut: Mutating residue number 91 from chain D (valine) into lysine (00:02:55)
[INFO] AutoMut: Mutating residue number 19 from chain D (leucine) into lysine (00:02:57)
[INFO] AutoMut: Mutating residue number 19 from chain D (leucine) into aspartic acid (00:03:09)
[INFO] AutoMut: Mutating residue number 104 from chain D (methionine) into glutamic acid (00:03:13)
[INFO] AutoMut: Mutating residue number 19 from chain D (leucine) into arginine (00:03:18)
[INFO] AutoMut: Mutating residue number 104 from chain D (methionine) into aspartic acid (00:03:19)
[INFO] AutoMut: Mutating residue number 104 from chain D (methionine) into lysine (00:03:20)
[INFO] AutoMut: Mutating residue number 104 from chain D (methionine) into arginine (00:03:24)
[INFO] AutoMut: Mutating residue number 92 from chain D (isoleucine) into glutamic acid (00:03:27)
[INFO] AutoMut: Mutating residue number 92 from chain D (isoleucine) into aspartic acid (00:03:30)
[INFO] AutoMut: Mutating residue number 23 from chain D (methionine) into glutamic acid (00:03:33)
[INFO] AutoMut: Mutating residue number 92 from chain D (isoleucine) into lysine (00:03:34)
[INFO] AutoMut: Mutating residue number 92 from chain D (isoleucine) into arginine (00:03:41)
[INFO] AutoMut: Mutating residue number 23 from chain D (methionine) into lysine (00:03:43)
[INFO] AutoMut: Mutating residue number 23 from chain D (methionine) into aspartic acid (00:03:55)
[INFO] AutoMut: Mutating residue number 94 from chain D (leucine) into glutamic acid (00:03:58)
[INFO] AutoMut: Mutating residue number 94 from chain D (leucine) into aspartic acid (00:03:58)
[INFO] AutoMut: Mutating residue number 23 from chain D (methionine) into arginine (00:04:02)
[INFO] AutoMut: Mutating residue number 94 from chain D (leucine) into lysine (00:04:08)
[INFO] AutoMut: Mutating residue number 94 from chain D (leucine) into arginine (00:04:09)
[INFO] AutoMut: Effect of mutation residue number 91 from chain D (valine) into glutamic
acid: Energy difference: 0.2004 kcal/mol, Difference in average score from
the base case: -0.0767 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 91 from chain D (valine) into lysine:
Energy difference: -0.7042 kcal/mol, Difference in average score from the
base case: -0.0710 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 91 from chain D (valine) into aspartic
acid: Energy difference: 0.5348 kcal/mol, Difference in average score from
the base case: -0.0936 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 91 from chain D (valine) into arginine:
Energy difference: -0.8487 kcal/mol, Difference in average score from the
base case: -0.0724 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 19 from chain D (leucine) into glutamic
acid: Energy difference: 0.6616 kcal/mol, Difference in average score from
the base case: -0.0921 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 19 from chain D (leucine) into lysine:
Energy difference: 0.3468 kcal/mol, Difference in average score from the
base case: -0.0760 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 19 from chain D (leucine) into aspartic
acid: Energy difference: 1.1672 kcal/mol, Difference in average score from
the base case: -0.0985 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 19 from chain D (leucine) into arginine:
Energy difference: 0.3870 kcal/mol, Difference in average score from the
base case: -0.0960 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 104 from chain D (methionine) into
glutamic acid: Energy difference: -0.6722 kcal/mol, Difference in average
score from the base case: -0.0664 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 104 from chain D (methionine) into
lysine: Energy difference: -0.3371 kcal/mol, Difference in average score
from the base case: -0.0654 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 104 from chain D (methionine) into
aspartic acid: Energy difference: 0.0525 kcal/mol, Difference in average
score from the base case: -0.0675 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 104 from chain D (methionine) into
arginine: Energy difference: -0.4595 kcal/mol, Difference in average score
from the base case: -0.0690 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 92 from chain D (isoleucine) into
glutamic acid: Energy difference: 3.2620 kcal/mol, Difference in average
score from the base case: -0.0126 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 92 from chain D (isoleucine) into lysine:
Energy difference: 0.4094 kcal/mol, Difference in average score from the
base case: -0.0087 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 92 from chain D (isoleucine) into
aspartic acid: Energy difference: 4.2518 kcal/mol, Difference in average
score from the base case: -0.0175 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 92 from chain D (isoleucine) into
arginine: Energy difference: 0.6939 kcal/mol, Difference in average score
from the base case: -0.0325 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 23 from chain D (methionine) into
glutamic acid: Energy difference: 0.9084 kcal/mol, Difference in average
score from the base case: -0.0491 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 23 from chain D (methionine) into lysine:
Energy difference: 0.2312 kcal/mol, Difference in average score from the
base case: -0.0438 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 23 from chain D (methionine) into
aspartic acid: Energy difference: 0.9886 kcal/mol, Difference in average
score from the base case: -0.0422 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 23 from chain D (methionine) into
arginine: Energy difference: 0.3302 kcal/mol, Difference in average score
from the base case: -0.0686 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 94 from chain D (leucine) into glutamic
acid: Energy difference: 0.9274 kcal/mol, Difference in average score from
the base case: -0.0625 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 94 from chain D (leucine) into lysine:
Energy difference: 0.5324 kcal/mol, Difference in average score from the
base case: -0.0724 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 94 from chain D (leucine) into aspartic
acid: Energy difference: 0.8921 kcal/mol, Difference in average score from
the base case: -0.0730 (00:04:30)
[INFO] AutoMut: Effect of mutation residue number 94 from chain D (leucine) into arginine:
Energy difference: 0.5455 kcal/mol, Difference in average score from the
base case: -0.0907 (00:04:30)
[INFO] Main: Simulation completed successfully. (00:04:34)
|
The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan4D score | mutation |
|---|---|---|---|---|
| 3 | T | D | -0.7120 | |
| 4 | S | D | -1.0924 | |
| 5 | S | D | -1.5189 | |
| 6 | S | D | -1.5191 | |
| 7 | T | D | -1.5080 | |
| 8 | K | D | -2.5024 | |
| 9 | K | D | -2.6513 | |
| 10 | T | D | -1.8086 | |
| 11 | Q | D | -1.5019 | |
| 12 | L | D | -1.0508 | |
| 13 | Q | D | -1.2205 | |
| 14 | L | D | 0.0000 | |
| 15 | E | D | -1.1730 | |
| 16 | H | D | -0.7706 | |
| 17 | L | D | 0.0000 | |
| 18 | L | D | 0.0513 | |
| 19 | L | D | 0.9301 | |
| 20 | D | D | 0.2007 | |
| 21 | L | D | 0.0000 | |
| 22 | Q | D | -0.2229 | |
| 23 | M | D | 0.2297 | |
| 24 | I | D | 0.0000 | |
| 25 | L | D | -0.7488 | |
| 26 | N | D | -1.4334 | |
| 27 | G | D | 0.0000 | |
| 28 | I | D | 0.0000 | |
| 29 | N | D | -1.3649 | |
| 30 | N | D | -1.1192 | |
| 31 | Y | D | 0.0366 | |
| 32 | K | D | -1.5815 | |
| 33 | N | D | 0.0000 | |
| 34 | P | D | -1.1789 | |
| 35 | K | D | -1.5016 | |
| 36 | L | D | -0.9371 | |
| 37 | T | D | -1.0202 | |
| 38 | R | D | -1.7508 | |
| 39 | M | D | 0.0000 | |
| 40 | L | D | -0.4053 | |
| 41 | T | D | -0.5029 | |
| 42 | F | D | -0.4613 | |
| 43 | K | D | -1.2913 | |
| 44 | F | D | 0.0000 | |
| 45 | Y | D | -0.3705 | |
| 46 | M | D | 0.0000 | |
| 47 | P | D | 0.0000 | |
| 48 | K | D | -3.0665 | |
| 49 | K | D | -2.9105 | |
| 50 | A | D | -2.1325 | |
| 51 | T | D | -1.5643 | |
| 52 | E | D | -2.4374 | |
| 53 | L | D | -1.5876 | |
| 54 | K | D | -1.9901 | |
| 55 | H | D | -1.8321 | |
| 56 | L | D | 0.0000 | |
| 57 | Q | D | -0.9277 | |
| 58 | C | D | 0.0000 | |
| 59 | L | D | 0.0000 | |
| 60 | E | D | -1.3797 | |
| 61 | E | D | -2.2643 | |
| 62 | E | D | 0.0000 | |
| 63 | L | D | 0.0000 | |
| 64 | K | D | -2.8125 | |
| 65 | P | D | -1.9596 | |
| 66 | L | D | 0.0000 | |
| 67 | E | D | -2.6907 | |
| 68 | E | D | -2.6160 | |
| 69 | V | D | 0.0000 | |
| 70 | L | D | 0.0000 | |
| 71 | N | D | -1.8532 | |
| 72 | L | D | -0.5475 | |
| 73 | A | D | -0.9606 | |
| 74 | Q | D | -1.3992 | |
| 75 | S | D | -1.8527 | |
| 76 | K | D | -2.3758 | |
| 77 | N | D | -2.0793 | |
| 78 | F | D | -0.7496 | |
| 79 | H | D | -1.8367 | |
| 80 | L | D | -1.7327 | |
| 81 | R | D | -3.0913 | |
| 82 | P | D | 0.0000 | |
| 83 | R | D | -3.5359 | |
| 84 | D | D | -3.3533 | |
| 85 | L | D | 0.0000 | |
| 86 | I | D | 0.0000 | |
| 87 | S | D | -1.2735 | |
| 88 | N | D | -1.0005 | |
| 89 | I | D | 0.0000 | |
| 90 | N | D | -0.1172 | |
| 91 | V | D | 1.2696 | |
| 92 | I | D | 0.2543 | |
| 93 | V | D | 0.0000 | |
| 94 | L | D | 0.1638 | |
| 95 | E | D | -1.1384 | |
| 96 | L | D | 0.0000 | |
| 97 | K | D | -1.6719 | |
| 98 | G | D | -1.5349 | |
| 99 | S | D | -1.6031 | |
| 100 | E | D | -2.1723 | |
| 101 | T | D | -1.0010 | |
| 102 | T | D | -0.4928 | |
| 103 | F | D | -0.0249 | |
| 104 | M | D | 0.8140 | |
| 105 | C | D | -0.6980 | |
| 106 | E | D | -1.5731 | |
| 107 | Y | D | -1.2611 | |
| 108 | A | D | -2.1752 | |
| 109 | D | D | -2.7953 | |
| 110 | E | D | -2.7924 | |
| 111 | T | D | -1.5131 | |
| 112 | A | D | 0.0000 | |
| 113 | T | D | -0.6219 | |
| 114 | I | D | 0.0000 | |
| 115 | V | D | -1.0896 | |
| 116 | E | D | -1.9681 | |
| 117 | F | D | 0.0000 | |
| 118 | L | D | 0.0000 | |
| 119 | N | D | -1.7099 | |
| 120 | R | D | -1.6022 | |
| 121 | W | D | 0.0000 | |
| 122 | I | D | -0.7514 | |
| 123 | T | D | -0.7846 | |
| 124 | F | D | 0.0000 | |
| 125 | A | D | 0.0000 | |
| 126 | Q | D | -1.1630 | |
| 127 | S | D | -0.8082 | |
| 128 | I | D | 0.0000 | |
| 129 | I | D | -0.5344 | |
| 130 | S | D | -0.4093 | |
| 131 | T | D | -0.1700 | |
| 132 | L | D | -0.2621 | |
| 133 | T | D | -0.2694 |
Automated mutations analysis - charged mutations
In the automated mutations mode, the server selects aggregation prone resides
and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine.
The table below shows 2 best scored mutants for each mutated residue. Protein variants
are ordered according to the mutation effect they had on protein stability
(energetic effect) together with the difference in the average per-residue aggregation score
between the wild type and the mutant (in the table green values indicate a positive change,
grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this
CSV file .
Mutant |
Energetic effect |
Score comparison |
|||
| VR91D | -0.8487 | -0.0724 | View | CSV | PDB |
| VK91D | -0.7042 | -0.071 | View | CSV | PDB |
| ME104D | -0.6722 | -0.0664 | View | CSV | PDB |
| MR104D | -0.4595 | -0.069 | View | CSV | PDB |
| LR19D | 0.387 | -0.096 | View | CSV | PDB |
| LK19D | 0.3468 | -0.076 | View | CSV | PDB |
| MR23D | 0.3302 | -0.0686 | View | CSV | PDB |
| MK23D | 0.2312 | -0.0438 | View | CSV | PDB |
| LR94D | 0.5455 | -0.0907 | View | CSV | PDB |
| LK94D | 0.5324 | -0.0724 | View | CSV | PDB |
| IR92D | 0.6939 | -0.0325 | View | CSV | PDB |
| IK92D | 0.4094 | -0.0087 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine